Bipolar disorder is a mood disorder characterized by at least one episode of mania or at least one period of severe depression plus one period of mild mania (hypomania or bipolar II) or severe mania (bipolar I). The pathogenic mechanisms at work are not fully understood although one can assume that it is multifactorial and multigenetic. Protein profiles of micropunched samples (1 mm) from cryostat-cut slices (300 mm thick) from Layers II and III from the frontal cortex (Brodmann Area 10) in deceased patients with bipolar disorder were analyzed by 2-D gel electrophoresis (2-DE) and mass spectroscopy (MS). The analysis revealed proteins over the pI range of 4-7, and a molecular weight range of ca. 100 Da-10 kDa. The 2-DE gel contained approximately 1000 proteins, which were detectable by silver staining. All silver stained features were identified by MALDI-TOF MS of tryptic peptides. The proteins whose abundance was reduced were identified as heat-shock protein 70, voltage-dependent calcium channel gamma-7 subunit, septin 2 (NEDD 5 protein homolog), macrophage scavenger receptor types I and II (CD204 antigen), and TFIH basal transcription factor complex p34 subunit. It could also be shown, by immunohistochemistry on the contralateral side, that some of the proteins were reduced in bipolar disorder. Furthermore, some of the data could be corroborated at the gene expression level of the same cases as well as in other brain regions of other cases using the Stanley Medical Research Institute Microarray Database. This is the first study to report on layer-specific changes at the protein level showing involvement of various regulatory and transcription systems including chaperone, calcium channel, transcription, and inflammatory pathways. We suggest that this section-based layer-specific proteomic approach to the analysis of major brain disorders is superior to the brain-block approach. This analysis showed that a variety of regulatory pathways are changed in bipolar disorder and might constitute a target for the development of therapeutic drugs.